Transport from the wild rapidly alters the diversity and composition of skin microbial communities and antifungal taxa in spring peeper frogs

Autor: Lauren P. Kane, William G. Van Bonn, Francis J. Oliaro, Christian F. Edwardson, Malissa Smith, Lee J. Pinnell

Publikováno v: Frontiers in Microbiomes, Vol 3 (2024)

Amphibians are routinely collected from the wild and added into managed care and public display facilities; however, there is a gap in understanding how these practices might alter the diversity and composition of skin microbial communities on these

Externí odkaz: https://doaj.org/article/55fb4735807b416e8815e85818c0c6cd

Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake

Autor: Christian F. Edwardson, James T. Hollibaugh

Publikováno v: Frontiers in Microbiology, Vol 9 (2018)

We compared the composition of microbial communities obtained by sequencing 16S rRNA gene amplicons with taxonomy derived from metatranscriptomes from the same samples. Samples were collected from alkaline, hypersaline Mono Lake, California, USA at f

Externí odkaz: https://doaj.org/article/f4da58ec11294560a395bb47cf3c1e25

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Autor: Fernando Vargas, Matthew R. Dillon, Stephanie B. Orchanian, Mary L. Preuss, Daniel McDonald, Christian C. Abnet, J. Gregory Caporaso, Alexey V. Melnik, Claire Duvallet, Massoud Maher, Max von Hippel, Colin J. Brislawn, Jamie Morton, Kyle C. Weber, Patrick Rosenthal, Qiyun Zhu, Lauren J. McIver, Talima Pearson, Clarisse Marotz, Madeleine Ernst, Ruth E. Ley, Jiarong Guo, Tomasz Kosciolek, Jorden Kreps, Benjamin D. Kaehler, Deanna L. Gibson, Yilong Zhang, Kestrel Gorlick, Catherine A. Lozupone, Nicholas A. Bokulich, Jessica L. Metcalf, Daniel M. Durall, Paul Keim, Daniel Petras, Elmar Pruesse, Dan Knights, Emily K. Cope, Gavin M. Douglas, Sean M. Gibbons, Hannes Holste, Austin D. Swafford, Yong-Xin Liu, Sabah Ul-Hasan, Joslynn S. Lee, Benjamin J. Callahan, Mehrbod Estaki, Zhenjiang Zech Xu, Jordan E. Bisanz, Jennifer Fouquier, Lingjing Jiang, Justin J. J. van der Hooft, Ahmad Turan Naimey, Michael S. Robeson, Harriet Alexander, Jesse R. Zaneveld, Andrés Mauricio Caraballo-Rodríguez, Gavin A. Huttley, Antonio Gonzalez, Curtis Huttenhower, Anupriya Tripathi, Pauline Trinh, Mingxun Wang, Emily Vogtmann, Susan Holmes, Yunhu Wan, Rashmi Sinha, Irina Koester, William A. Walters, Yang Bai, Kyo Bin Kang, Luke R. Thompson, Christian F. Edwardson, Ricardo Silva, Pedro J. Torres, Gabriel A. Al-Ghalith, Stefan Janssen, Kyle Bittinger, Manimozhiyan Arumugam, Jonathan Warren, Alan K. Jarmusch, Lasse Buur Rasmussen, Rob Knight, Se Jin Song, Michael Shaffer, Sydney C. Morgan, Bryan D Martin, Peter J. Turnbaugh, C. Titus Brown, Jose A. Navas-Molina, Morgan G. I. Langille, Christopher R. Keefe, Benjamin Hillmann, Eric J. Alm, Evan Bolyen, Arron Shiffer, Louis-Félix Nothias, Christian Diener, Nicola Segata, Francesco Asnicar, Charles H. D. Williamson, Samuel L. Peoples, Amy D. Willis, Pieter C. Dorrestein, Adam R. Rivers, John Chase, Scott T. Kelley, Julia M. Gauglitz, Yoshiki Vázquez-Baeza, John R. Spear, Jai Ram Rideout, Asker Daniel Brejnrod, Erikka Loftfield

Publikováno v: Nature Biotechnology 37 (2019) 8
Nature Biotechnology
Nature Biotechnology, 37(8), 852-857
PMC

QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Slo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f54f79979681348f38899868524602c4
https://research.wur.nl/en/publications/reproducible-interactive-scalable-and-extensible-microbiome-data-

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Autor: Jamie Morton, Ruth E. Ley, Samuel L. Peoples, Dan Knights, Yong-Xin Liu, Gavin M. Douglas, Colin J. Brislawn, Fernando Vargas, Yunhu Wan, Daniel McDonald, Sean M. Gibbons, Daniel Petras, Amy D. Willis, Stephanie B. Orchanian, Rashmi Sinha, J. Gregory Caporaso, Gabriel A. Al-Ghalith, Claire Duvallet, Adam R. Rivers, Kyo Bin Kang, Lasse Buur Rasmussen, Pieter C. Dorrestein, Benjamin J. Callahan, Michael Shaffer, Rob Knight, Patrick Rosenthal, Madeleine Ernst, Matthew R. Dillon, Christian F. Edwardson, Qiyun Zhu, Yang Bai, Alexey V. Melnik, Daniel M. Durall, Christian C. Abnet, Lauren J. McIver, Julia M. Gauglitz, Jiarong Guo, Joslynn S. Lee, Charles H. D. Williamson, Tomasz Kosciolek, Massoud Maher, Emily Vogtmann, Mary L. Preuss, Kyle Bittinger, Alan K. Jarmusch, Mingxun Wang, Jose A. Navas-Molina, Susan Holmes, Michael S. Robeson, Manimozhiyan Arumugam, C. Titus Brown, Zhenjiang Zech Xu, Harriet Alexander, Nicola Segata, John Chase, Francesco Asnicar, Se Jin Song, Yoshiki Vázquez-Baeza, Sydney C. Morgan, Austin D. Swafford, Justin J. J. van der Hooft, Irina Koester, Stefan Janssen, Ahmad Turan Naimey, Antonio Gonzalez, Jessica L. Metcalf, Gavin A. Huttley, Elmar Pruesse, Scott T. Kelley, Jonathan Warren, Talima Pearson, Anupriya Tripathi, Luke R. Thompson, Sabah Ul-Hasan, Peter J. Turnbaugh, Emily K. Cope, Christopher R. Keefe, Hannes Holste, Catherine A. Lozupone, Ricardo Silva, Pedro J. Torres, Max von Hippel, Eric J. Alm, Evan Bolyen, Jordan E. Bisanz, Lingjing Jiang, Louis-Félix Nothias, Andrés Mauricio Caraballo-Rodríguez, William A. Walters, Curtis Huttenhower, Clarisse Marotz, Kyle C. Weber, Yilong Zhang, Kestrel Gorlick, Paul Keim, Asker Daniel Brejnrod, Deanna L. Gibson, Morgan G. I. Langille, Jennifer Fouquier, Jesse R. Zaneveld, Benjamin Hillmann, Mehrbod Estaki, John R. Spear, Jai Ram Rideout, Jorden Kreps, Benjamin D. Kaehler, Pauline Trinh, Nicholas A. Bokulich, Erikka Loftfield, Bryan D Martin, Arron Shiffer, Christian Diener

Publikováno v: Nature Biotechnology (2019)
Nature Biotechnology

In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ba38ad653e9de0b61f094bb9542ef7f9
https://doi.org/10.1038/s41587-019-0252-6

Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China

Autor: Christian F. Edwardson, Geng Wu, Stephen R. Quake, Iwijn De Vlaminck, Hailiang Dong, Qiuyuan Huang, Brandon R. Briggs, Hongchen Jiang

Publikováno v: PLoS ONE, Vol 9, Iss 11, p e111681 (2014)
PLoS ONE

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonm

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::affc9664094c50a15de79bdc7fb4f22a
http://europepmc.org/articles/PMC4218802?pdf=render